Contacts of the strand formed by residues 487 - 498 (chain C) in PDB entry 6Q0R
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 487 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480C GLU 4.0 0.9 - - - +
481C VAL* 3.5 2.5 - - - +
482C CYS* 2.8 36.7 + - + +
485C THR* 3.5 33.5 + - - +
486C ASN* 1.3 77.1 - - - +
488C VAL* 1.3 64.2 - - - +
489C LEU 4.0 0.8 + - - -
520C ALA* 4.3 22.2 - - + +
521C TRP 3.4 3.8 - - - +
522C ASP* 4.0 28.6 + - - +
529C GLU* 5.3 6.2 + - - +
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Residues in contact with VAL 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B LEU* 3.8 30.3 - - + -
251B LEU* 4.1 12.6 - - + -
478C ILE* 4.0 17.0 - - + -
480C GLU 3.6 3.1 - - - +
481C VAL* 4.5 7.6 - - + -
487C GLN* 1.3 77.0 - - - +
489C LEU* 1.3 60.3 + - - +
490C ILE* 3.7 24.7 + - + +
519C VAL 3.6 2.1 - - - +
520C ALA* 3.5 2.0 - - - -
521C TRP* 2.7 49.3 + - + +
523C LEU* 3.9 24.5 - - + -
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Residues in contact with LEU 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478C ILE* 3.6 2.9 - - - +
479C LEU* 2.7 59.2 + - + -
480C GLU* 2.8 34.4 + - + +
487C GLN 4.0 1.2 - - - -
488C VAL* 1.3 69.9 - - - +
490C ILE* 1.3 55.9 + - - +
518C LYS* 4.7 5.8 - - + -
519C VAL 3.7 12.6 - - - +
520C ALA* 4.5 7.9 - - + +
531C VAL* 3.6 30.5 - - + -
558C MET* 6.3 1.8 - - + -
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Residues in contact with ILE 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B LEU* 4.1 11.9 - - + -
448C LEU* 4.2 23.6 - - + -
450C PHE* 4.3 8.1 - - + -
453C VAL* 5.8 1.3 - - + -
476C ILE* 3.7 27.6 - - + -
477C VAL 3.8 2.5 - - - +
478C ILE* 4.0 18.6 - - + -
479C LEU* 4.9 2.0 - - - -
488C VAL* 3.8 25.8 - - + +
489C LEU* 1.3 74.4 - - - +
491C ASN* 1.3 59.7 + - - +
492C ILE* 3.8 21.1 - - + -
517C LEU 3.7 1.2 - - - +
518C LYS* 3.5 3.3 - - - +
519C VAL* 2.9 51.1 + - + +
521C TRP* 5.5 2.0 - - + -
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Residues in contact with ASN 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476C ILE* 3.4 5.9 - - - +
477C VAL 2.9 31.2 + - - +
479C LEU* 3.7 20.2 - - + +
490C ILE* 1.3 72.2 - - - +
492C ILE* 1.3 68.9 + - - +
516C SER* 2.7 24.2 + - - -
517C LEU 3.6 5.4 - - - +
518C LYS* 3.5 27.1 - - - +
551C TYR* 2.9 28.1 + - - +
554C SER* 4.9 3.6 + - - -
555C CYS* 3.4 24.3 - - - +
558C MET* 5.5 0.8 - - - -
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Residues in contact with ILE 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450C PHE* 5.5 2.5 - - + -
453C VAL* 4.3 13.9 - - + -
454C ILE* 3.8 28.0 - - + -
475C ASP 3.7 2.5 - - - -
476C ILE* 3.5 28.9 - - + -
490C ILE* 3.8 24.0 - - + -
491C ASN* 1.3 75.6 + - - +
493C GLY* 1.3 68.0 + - - +
494C LEU* 3.7 5.5 + - + +
515C THR 3.6 0.7 - - - +
516C SER* 3.4 4.0 - - - -
517C LEU* 2.8 60.5 + - + +
519C VAL* 4.0 21.5 - - + -
551C TYR* 3.6 0.9 - - - -
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Residues in contact with GLY 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474C TYR* 3.1 10.9 - - - +
475C ASP 2.8 32.5 + - - -
492C ILE* 1.3 72.1 - - - +
494C LEU* 1.3 58.3 + - - +
514C HIS* 4.1 0.4 - - - -
515C THR 3.6 4.3 - - - -
548C TRP* 3.5 16.2 - - - -
551C TYR* 3.0 28.2 + - - -
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Residues in contact with LEU 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454C ILE* 3.6 40.6 - - + -
458C ILE* 3.8 9.9 - - + -
471C PHE* 4.1 19.7 - - + -
473C ASP 4.0 2.2 - - - +
474C TYR* 3.7 25.1 - - + -
492C ILE* 4.3 6.7 - - + +
493C GLY* 1.3 72.6 - - - +
495C LEU* 1.3 61.1 + - - +
496C LEU* 3.7 25.3 + - + +
513C TYR 3.8 0.5 - - - +
514C HIS* 3.1 15.7 + - - -
515C THR* 2.9 46.5 + - + +
517C LEU* 4.4 6.7 - - + -
548C TRP* 3.9 2.2 - - - -
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Residues in contact with LEU 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471C PHE* 3.4 7.0 - - - +
472C SER* 2.7 45.2 + - - +
473C ASP* 3.3 21.6 + - + +
494C LEU* 1.3 71.6 - - - +
496C LEU* 1.3 55.7 + - - +
512C THR* 3.8 22.0 - - + -
513C TYR 3.6 13.0 - - - +
514C HIS* 4.9 1.3 - - + -
539C VAL* 4.3 17.5 - - + -
544C SER* 5.0 11.7 - - - +
547C VAL* 4.0 20.4 - - + -
548C TRP* 3.7 31.5 - - + +
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Residues in contact with LEU 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458C ILE* 4.9 0.2 - - + -
464C TRP* 3.8 28.3 - - + -
468C PHE* 3.9 14.4 - - + -
470C SER 3.4 13.2 - - - +
471C PHE* 4.0 3.1 - - + +
494C LEU* 3.7 24.9 - - + +
495C LEU* 1.3 74.1 - - - +
497C LEU* 1.3 70.0 + - - +
498C ALA* 3.8 25.1 - - + -
512C THR* 3.3 9.2 - - - +
513C TYR* 3.0 46.4 + - + +
515C THR* 3.9 11.0 - - + -
536C LEU* 3.9 15.7 - - + -
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Residues in contact with LEU 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468C PHE* 3.9 1.4 - - - -
469C CYS* 2.8 40.7 + - + -
470C SER* 2.8 36.1 + - - +
471C PHE 4.9 0.4 - - - -
472C SER* 3.6 20.6 - - - +
496C LEU* 1.3 79.6 - - - +
498C ALA* 1.3 57.7 + - - +
510C PRO* 5.6 7.4 - - + -
511C LYS 3.4 8.7 - - - +
512C THR* 5.3 10.5 - - + +
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Residues in contact with ALA 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467C GLN* 3.1 22.2 - - + +
468C PHE* 3.9 2.9 - - - -
469C CYS* 4.1 3.8 - - - -
496C LEU* 3.8 17.3 - - + -
497C LEU* 1.3 75.8 - - - +
499C PHE* 1.3 65.7 + - - +
510C PRO* 4.2 4.0 - - - +
511C LYS 2.8 35.2 + - - +
513C TYR* 3.4 7.8 - - + -
536C LEU* 4.0 15.9 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il